...

To import the matrices into Partek Flow, create a new project and click Import data > Import single cell data.

Navigate to the folder containing your filtered matrices. By default, the Cell Ranger pipeline output will have a folder called filtered_gene_bc_matrices.

...

Specify the annotation file used when running the pipeline. If desired, the sample name can also be modified. 

...

The Cell Ranger pipeline can also generate the same filtered gene barcode matrix in h5 format. This gives you the ability to select just one file per matrix and select multiple matrices to import in batch. To import an h5 matrix, simply select the h5 file when selecting a file for import and click Next. This will take you to the same configuration page shown in Figure 4.

This feature is also useful for importing multiple samples in batch. Simply put all h5 files from your experiment on a single folder, navigate to the folder and select all the matrices you would like to import.

Configure all the relevant sample metadata, including sample name and the annotation that was used to generate the matrices, and click Finish when completed. Note that all matrices must have been generated using the same reference genome and annotation to be imported into the same project.

...